What I am wondering is if stuff that I download via apt does it not stay after a restart? I have dsl on my flash, is that what matters? Just because right after I restarted I didn't have any of the programs I had prior to the restart. Now my guess is that is why myDSL exists right? Or am I just screwing up? Thanks

update, after a restart I noticed that the stuff I downloaded with myDSL is gone to. Does that only work with an hd install?

Save your mydsl extensions to another partition besides the filesystem partition if you want them to be saved after reboot. As for programs installed with apt-get they will be gone after reboot so you need to either backup or use the deb2dsl script and create your own extensions.